QIIME (canonically pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to studies based on billions of sequences from thousands of samples.
Installing: The quickest way to get started using QIIME is with MacQIIME (if you're running Mac OS X), qiime-delpoy (if you're using Linux), or the Amazon EC2 image or VirtualBox (if you're using Windows, Mac OS X, or Linux).
Running: Once you've installed QIIME, move on to the QIIME Tutorials. The Illumina overview tutorial is a good first analysis to run. In this tutorial you'll download a small data set and work through a series of commands that will introduce you to some of QIIME's commonly used features and analyses.
Getting help: We provide support for QIIME on the QIIME Forum. Before requesting help with QIIME on the forum, please review this post. We devote a lot of time to helping users on the forum, and reviewing that post will help us to efficiently help you, leaving us with more time for QIIME development and our own research.
For getting started on interacting with the command line, please review this post.
QIIME scripts: As you become more proficient with QIIME, the QIIME script documentation will help you explore and learn QIIME's functionality.
QIIME is open source software. You can find the code under public revision control in our GitHub repository. You can find related projects under the QIIME organization on GitHub. We're very interested in community contributions and feedback. Use pull requests to contribute code or documentation, and our issue tracker to report bugs or request new features.
QIIME-deploy: Install QIIME easily on Ubuntu and RedHat Linux.
MacQIIME: Easy install of QIIME on MacOS X.
Bio-Linux: QIIME and hundreds of other bioinformatics tools in an Ubuntu-based Linux distribution.
n3phele: Run QIIME on the Amazon Cloud from a web interface - no command line interaction is required.
If you use QIIME for any published research, please include the following citation:
QIIME allows analysis of high-throughput community sequencing data
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303
QIIME wraps many other software packages, and these should be cited if they are used. For example, users of pick_de_novo.py are actually using QIIME, uclust, RDP classifier, PyNAST, and FastTree, since QIIME is wrapping those applications. Any time you're using tools that QIIME wraps, it is essential to cite those tools. The Werner Lab website has a list of software, including citations, that is used in the various stages of QIIME.